1. Can you please briefly summarize the paper? 

Our study centers on hepatocellular carcinoma, which is the most prevalent form of liver cancer, ranking as the sixth most common and third most lethal cancer globally. Despite advancements in treatment modalities, the prognosis of HCC remains bleak due to its heterogeneity. Hence, we aimed to develop a novel gene set and AI tool to identify malignant hepatocytes in scRNA-seq data, thereby addressing the lack of existing biomarkers and computational tools and contributing to the discovery of therapeutic targets.

Utilizing largely integrated scRNA-seq data, we identified 113 genes significantly upregulated in malignant hepatocytes, which make up our HepScope gene set, and validated its capacity to distinguish tumor cells in multi-omics data. In addition, we investigated the biological functions and roles of these genes in tumor sites by conducting multiple analyses, including GO, KEGG, tumor immune microenvironment, cell-cell interaction, and survival analyses. Moreover, we opted to apply the 1D-CNN model for even more precise classification, as we observed structural similarities between ECG data and the gene expression matrix from scRNA-seq data. Benchmarking against five other HCC-related gene sets and 11 AI or ML models demonstrated that the HepScope-trained model surpassed the alternative models, as supported by its superior evaluation metrics, including time consumption.

Ultimately, the HepScope gene set, featuring 113 genes, represents a significant advancement in understanding the complexities of HCC. Its utility extends beyond the identification of malignant hepatocytes, encompassing prognostication and comprehensive characterization of the tumor immune microenvironment. Moreover, our study pioneered the use of a convolutional neural network model for gene expression analysis.

2. Can you please tell us the main difficulties you had in the laboratory work and how you overcame them?

The most challenging aspect of this project was thinking creatively. As the project progressed, I realized I needed to come up with innovative solutions to achieve publication. Initially, I relied heavily on guidance from my professors and senior colleagues, as I was comfortable following established directions. However, I eventually decided to be proactive in applying AI techniques into our research, despite having no prior experience with them.?This decision introduced a new set of challenges, particularly because our focus was primarily on data analysis. I had to extensively research and troubleshoot online to resolve errors in the AI model. This period was particularly difficult for me, as I often blamed myself for the setbacks. At times, I even considered quitting my degree, questioning whether I was truly capable of conducting research in the lab. However, with the encouragement and support of my lab mates and professor, I gradually regained confidence and ultimately succeeded in completing the project.

3. Please introduce your laboratory, university or organization to bio-researchers in Korea.

I firmly believe that our lab is the best laboratory in South Korea for several reasons. First and foremost, there is a distinctive absence of the hierarchy. We foster a collaborative environment where everyone supports and encourages each other. The kindness, warmth, and empathy of my colleagues have been instrumental in helping me maintain my mental well-being and manage the frustrations that arise from frequent technical challenges throughout this project.

Another strength of our lab is its diverse international community, which includes students from five different nationalities. With my professor’s extensive international experience, we are encouraged to communicate effectively across cultures, which has not only enriched my interpersonal skills but also helped me improve my English. When I first joined the lab, my English was limited to basic phrases like “Hello,” “Thank you,” and “Okay,” but over time, I’ve gained much more confidence in both my communication and language abilities.

Additionally, our lab offers numerous opportunities for collaboration with pioneering researchers, both within South Korea and internationally. For instance, we have ongoing communication with the National Cancer Center in Singapore regarding our current research projects, which provides valuable exposure to cutting-edge work in the field.

Finally, our lab places a strong emphasis on independence. Each member typically manages their own projects and works with various collaborators, creating a collegial atmosphere where there is no sense of competition or jealousy, but rather mutual respect and support.

4. Please tell us your experiences and your thoughts related to research activities abroad.

Although I have not yet had the opportunity to conduct research abroad, my experiences attending international conferences have provided me with valuable insights. I’ve noticed that research activities in other countries tend to be more creative and expansive compared to those in Korea. In our local academic environment, there is a strong emphasis on data analysis, often driven by a societal intolerance of failure. This focus can sometimes stifle innovation and risk-taking. I believe that without the willingness to embrace failure, we risk stagnating in the field of science. Failure is an essential part of the learning process and a key driver of progress, as it has been throughout human history.

Moreover, I think the influence of Confucian culture in Korea makes us more hesitant to ask questions or seek advice, especially from those with less experience or younger colleagues. In contrast, at international conferences, I was struck by how freely professors and PhDs engaged in discussions, asking questions during presentations without concern for their status or affiliation. I was particularly surprised to see senior researchers presenting their own posters, which was a cultural difference that left a lasting impression on me.

These observations have motivated me to focus more deeply on my studies and strive to embody the qualities of a great researcher in the future-embracing both creativity and the lessons learned from failure.

5. Can you provide some advice for younger scientists who have plans to study abroad?

I consider myself to be younger than most researchers in Korea and the youngest member of my lab. As such, I prefer to share my personal experiences rather than offer advice, as I feel I am still in the early stages of my journey. Throughout my pursuit of a master’s degree, I’ve witnessed both myself and many others struggle with our research at various points.

There are times when it’s easy to feel isolated, as though no one can understand our challenges or offer the help we need. However, I have come to realize that no one can solve our problems for us, and that struggles are a part of the shared human experience. It’s important to persevere and keep pushing forward, even in difficult moments. As the saying goes, "God helps those who help themselves." This mindset has helped me stay resilient and motivated as I work to overcome the obstacles in my path.

6. Future plan?

I truly love my lab members and my PI, considering them family. I believe that most researchers in the bioinformatics fields possess similar abilities and skills for data analysis. However, it is difficult to ignore the enormous R&D funding provided by national governments, such as the US and China, which enables their researchers to conduct large-scale studies. Therefore, I aim to apply for a PhD in the US to gain more opportunities for extensive and comprehensive research. My ultimate goal is to demonstrate the biological processes that occur in our bodies by reducing the gap between real and sequencing data, thereby facilitating the investigation of human diseases.

7. Do you have anything else that you would like to tell Korean scientists and students?
As a graduate student and future scientist, I support and respect all of my colleagues. Without senior scientists, studying in this field would be impossible. Particularly, I would like to express my deepest gratitude to my professor, Su Bin Lim, who is not only one of my role models but also a great scientist. Her guidance and mentorship have been invaluable throughout my journey. Both my academic growth and personal development have been greatly influenced by her unwavering support, insightful advice, and exemplary leadership. It has truly been a privilege to join her lab and pursue my graduate studies under her direction. I consider myself fortunate to have had the opportunity to learn from such an inspiring and accomplished researcher.

The presence of fellow students in the sciences has been a constant source of support and inspiration, helping me maintain hope and stay focused on my path. I am especially grateful to my lab mates, whose collaboration, encouragement, and unwavering support have been invaluable in overcoming the challenges I’ve faced. My friends from my undergraduate have also played a crucial role in keeping me grounded and motivated. None of this would have been possible without the encouragement, and love of those around me, including my family. I will be grateful for the support I’ve received and am committed to paying it forward by helping others as much as I can.